rs1261078

Variant names:

• chr18-55199560-A-G
• rs1261078

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.153 in 152,156 control chromosomes in the GnomAD database, including 4,198 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (4198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.55
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23215 AN: 152038 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.00970

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23290 AN: 152156 Hom.: 4198 Cov.: 32 AF XY: 0.147 AC XY: 10945 AN XY: 74412

African (AFR) AF: 0.440 AC: 18217 AN: 41430

American (AMR) AF: 0.0716 AC: 1095 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4822

European-Finnish (FIN) AF: 0.00970 AC: 103 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0497 AC: 3380 AN: 68006

Other (OTH) AF: 0.120 AC: 253 AN: 2112

Alfa AF: 0.119 Hom.: 419

Bravo AF: 0.173

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Benign	0.67
PhyloP100		2.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1261078; hg19: chr18-52866791;